Summary

---
title: "COVID-19 Nepal"
output: 
  flexdashboard::flex_dashboard:
    orientation: rows
    social: menu
    source_code: embed
    vertical_layout: fill
---

```{r setup, include=FALSE}
### DEFINE LIBRARIES ---
library("flexdashboard")
library("plotly")

# DATA CURATED FROM DATA RELEASED (UPDATED DAILY) FROM
# GOVT. OF NEPAL, MINISTRY OF HEALTH AND POPULATION
# HEALTH SECTOR RESPONSE TO CORONAVIRUS DISEASE (COVID-19)
# URL: https://drive.google.com/drive/folders/1QhLMbT76t6Zu1sFy5qlB5aoDbHVAcnHx

### DEFINE FILE ---
file.dat <- file.path("data_total.tsv")

#------------------ Parameters ------------------
# Set colors
# https://www.w3.org/TR/css-color-3/#svg-color
test_color <- "#4292c6"
confirmed_color <- "#b15928"
active_color <- "#ff7f00"
recovered_color <- "#33a02c"
death_color <- "#e31a1c"

### LOAD DATA ---
dat <- read.delim(file.dat, header=TRUE, stringsAsFactors=FALSE)
dat$date <- as.Date(dat$date, format = "%m/%d/%y")

### FUNCTION: num_changes() ---
num_changes <- function(x){
  y <- numeric()
  y[1] <- x[1]
  
  for(i in 2:length(x)){
    y[i] <- x[i] - x[i-1]           
  }
  
  return(y)
}  

### CALCULATE ACTIVE INFECTION, NEW TESTS, NEW POITIVES, NEW DEATH, NEW RECOVERED ---
dat$active_case <- dat$total_positive - dat$total_recovered
dat$new_tested <- num_changes(dat$total_test)
dat$new_positive <- num_changes(dat$total_positive)	
dat$new_death <- num_changes(dat$total_death)	
dat$new_recovered <- num_changes(dat$total_recovered)

### LATEST INFO ---
total_test <- dat$total_test[nrow(dat)]
total_positive <- dat$total_positive[nrow(dat)]
active_case <- dat$active_case[nrow(dat)]
total_recovered <- dat$total_recovered[nrow(dat)]
total_death <- dat$total_death[nrow(dat)]

```


Summary
=======================================================================
Row
-----------------------------------------------------------------------

### Total Test Conducted {.value-box}

```{r}
valueBox(value = paste(format(total_test, big.mark = ","), "", sep = " "), 
         caption = "Total Test Conducted", 
         icon = "fas fa-vial", 
         color = test_color)
```

### Positive {.value-box}

```{r}
valueBox(value = paste(format(total_positive, big.mark = ","), "", sep = " "), 
         caption = "Positive Cases", 
         icon = "fas fa-user-md", 
         color = confirmed_color)
```


### active {.value-box}

```{r}
valueBox(value = paste(format(active_case, big.mark = ","), "", sep = " "), 
         caption = "Active Cases", 
         icon = "fas fa-ambulance", 
         color = active_color)
```

### recovered {.value-box}

```{r}
valueBox(value = paste(format(total_recovered, big.mark = ","), "", sep = " "),  
         caption = "Recovered Cases", icon = "fas fa-heartbeat", 
         color = recovered_color)
```

### death {.value-box}

```{r}
valueBox(value = paste(format(total_death, big.mark = ","), "", sep = " "),  
         caption = "Death Cases", 
         icon = "fas fa-bolt", 
         color = death_color)
```


Row
-----------------------------------------------------------------------

### Total Positive Cases in Nepal

```{r}
plotly::plot_ly(data = dat,
                x = ~ date,
                y = ~ total_positive,
                line = list(color = confirmed_color, width = 2),
                marker = list(color = confirmed_color, width = 4),
                name = 'Positive', 
                type = 'scatter',
                mode = 'lines+markers') %>%
plotly::layout(title = "",
                 yaxis = list(title = "Total Positive Cases"),
                 xaxis = list(title = "Date"),
                 legend = list(x = 0.1, y = 0.9),
                 hovermode = "compare")

```

Row {data-width=400}
-----------------------------------------------------------------------


### RT-PCR Tests Conducted
    
```{r}
plotly::plot_ly(data = dat,
                x = ~ date,
                y = ~ total_test,
                name = 'Positive', 
                type = 'scatter',
                mode = 'lines+markers') %>%
plotly::layout(title = "",
                 yaxis = list(title = "Total RT-PCR Test Conducted"),
                 xaxis = list(title = "Date"),
                 legend = list(x = 0.1, y = 0.9),
                 hovermode = "compare")
```


### Data
    
```{r}
dtbl <- dat %>%
          dplyr::select(Date=date, 
                        'Total Test'=total_test, 
                        'Total Positive'=total_positive,
                        'Active Cases'=active_case,
                        'Total Recovered'=total_recovered,
                        'Total Death'=total_death)

dtbl$Date <- as.Date(dtbl$Date, format = '%Y/%m/%d')

dtbl <- dtbl[order(dtbl$Date, decreasing = TRUE),]

dtbl %>%  
  DT::datatable(rownames = FALSE,
            options = list(searchHighlight = TRUE, 
                           pageLength = 20))
```